The Agent in the Anthropologist
by BluePuffBall
Summary: What if Brennan wasn't quite who she claimed to be? What if she had a dark past that was finally starting to catch up to her? Follow Bones as she faces her demons and realizes that there is more to life than logic. AU. Set after 5x22. M for gore. B/B.
1. Chapter 1

**_Disclaimer: Nothing's mine._**

**Chapter One**

Temperance "Bones" Brennan sat at her desk in the Jeffersonian as she stared at a skull. There was nothing odd about it. One thousand years old, a male somewhere in his thirties, Asian. It had all the markers of a bone that was from an ancient civilization. It was also the only thing she was really sure of at the moment.

For the past several years there had been many things that were constant, as certain as the rising sun. Seeley Booth, Angela Montenegro, Jack Hodgins, Camille Saroyan, and the Jeffersonian itself. Even Lance Sweets – though annoying – was a person she could not imagine not having in her life. They had become integral parts of her being in a very short amount of time. Now however it seemed that the team was splitting up.

Booth was heading off to Iraq to train young soldiers. The famous forensic anthropologist knew that this was a good thing. Her partner was one of the best and it was likely that the death rates would go down with his training.

Angela and Hodgins were going to Paris to relive the dream. Or that was what Angela was doing. Jack was just going with her because he loved his wife dearly.

Cam wasn't going anywhere really. She was staying in D.C. but was going back to being a state coroner instead a specialist at the Jeffersonian.

Sweets had broken it off with Daisy and it seemed to have broken something in him. He was taking a vacation from psychology. Brennan had no idea what he was going to be doing but she hoped that he would be happy. Even if he practiced a soft science.

As for herself, she was going to the Maluku Islands to study what could be a crucial link in the evolutionary chain of homo sapiens. Even though she was all packed and ready to go, Bones felt unsure of herself. She loved her job and this was the first time she was having doubts about gallivanting across the world to study remains. Why was that? Why was she having second thoughts _now_ of all times?

Temperance was shaken from her thoughts as her phone rang. She sighed wondering who would call her at eleven PM. Still picking up the phone was better then brooding about what her life had become. "Brennan here."

There was silence and she thought for a moment that it was a prank call. "Hello Athena."

As soon as she heard that name she felt cold inside, even though she knew her body temperature was still a toasty 37°C. "I'm afraid you have the wrong number –"

"I know I have the right number Athena. I know that you're retired. I know that you're going to the Maluku Islands. I also know that you don't know that someone's trying to kill you."

The man's voice – for it was definitely male – sounded familiar from a life she tried her best to forget. "Jason?"

"Yeah. It's Assistant Director Jason now though Athena."

It didn't surprise her that he was now near the top of command. He was good. Not as good as her, but still good. "Congratulations I suppose. And stop calling me that."

There was a dry chuckle. "No can do. Right now I'm not calling forensic anthropologist Temperance Brennan. I'm calling former Agent Athena Asheblade. The triple A as I used to fondly call you."

Bones let out an impatient sigh. "You still have the rambling problem Jason. Either tell me what's going on or leave me alone."

"And you haven't changed." He was silent for a moment before saying, "But you're right, I need to get to the point. The Agency needs you."

"Needs me? Why would it need me?"

"Hush and listen. You remember one of your last missions? The one with Drake?"

Brennan felt a wash of unwelcome memories come over her. A dark field. A tall man. A little girl with a gun to her head. "It is rather hard to forget something like that Jason." _Even if I wanted to._

"Yeah…Listen Drake had a son. He was only thirteen when Drake died. We had hoped that he wouldn't turn into a sociopath but it wasn't meant to be."

"So you're saying that Drake Jr. is a murderous twenty-seven year old. What does this have to do with me? As you said when you started this conversation, I'm _retired._"

Jason's voice was so soft that she had to strain to hear his next words. "He's a psychopath with a fixation on making those who hurt his father pay…Athena he's fixated on _you._"

The earlier chill was nothing compared to this freezing realization. It wasn't hard to connect the dots. She had killed his father and so he would want revenge. And if Drake Jr. was anything like Drake then he would come after everyone she cared about before hunting her down and slaughtering her like a dog. If she let him, that is.

"What do you want me to do, Jason? Come back? Return to the CIA and become Dark Angel Athena again?"

Her voice was filled with sorrow and no small amount of anger. _She_ was supposed to be retired. _She _wasn't supposed to be worried about sociopaths from her past.

"Yes, Athena, that's _exactly_ what I want you to do. And you have to, if you want your friends to live on in blissful unawareness about your past. Because we can't catch him Athena. Not without you. And if he isn't caught then Drake Jr. will come after your friends to get at you. And then they'd know."

Temperance Brennan was many things. She was calculating, fact based, and ignored her emotions. She had never been a cold blooded killer. Athena Asheblade, however, was a killer. _She _made intuitive leaps in logic, _she_ was _devoid _of emotions – since _she_ refused to recognize that _she_ had any – and _she_ killed without remorse or regret. Or at least, she had before she had become Dr. Brennan. Now she regretted every life that stained her hands red. But there was one thing that Athena and Temperance shared. The fact that that those she cared about would only be harmed over her dead body. And that was the only reason that the next few words spilled out of her mouth.

"Fine. Where do I need to go?"

"I knew you'd say yes…Go outside. There should be a black SUV waiting across the street. The sign is 'Dark Angel' and the counter sign is 'Athena Lives'."

Brennan snorted. "Wonderful. I never knew you were so creative Jason."

"Hey," He sounded offended. "Don't disrespect my creativity, when you don't have any!"

Just before she hung up Jason said one last thing. "Leave your phone in your office Athena. It's best if you just disappear while you're on this case."

Temperance Brennan disconnected the call and placed her phone on her desk. She looked around her office, with its glass walls, leather couches, and elegant desk, saying farewell to all that was familiar. Then she stood and walked out the door, not looking back. She knew that if she looked back that she would never have been able to leave.

As Bones exited the Jeffersonian for what could have been the last time she could only hope that they would be safe. Even if she died protecting them. When she gave the sign to the driver and heard the counter sign she could only snort. _Athena lives indeed. _As the SUV pulled away from the only world that the forensic Anthropologist should have known, Doctor Brennan became once again, Athena Asheblade, otherwise known as Dark Angel Athena. One of the best – and most heartless – agents that the CIA had ever seen.

* * *

><p><strong>I seem to enjoy starting new stories before finishing my other ones. If you hadn't noticed this story will be somewhat AU. Actually it'll be almost completely AU after season 5. I might get some things mixed up, because while I love <em>Bones<em> I haven't really watched it for a while. This will be M for gore, mature themes, and a smattering of language. This will also eventually have B/B. Eventually. Hopefully you liked the beginning of _The Agent in the Anthropologist._ Until next time...**


	2. Chapter 2

**_Disclaimer: Only the crazy plot bunnies are mine._**

**Chapter Two**

Seeley Booth wasn't having a good day. Hell, he wasn't having good past few months. After the entire fiasco with telling Bones that he loved her only to have her reject him, he had never really felt whole. Instead there was a gaping hole where his heart should have been but wasn't there. It had gone from bad to worse when he was contacted by the Army to train the new recruits how to kill.

Now – the night before he was scheduled to leave for Afghanistan – he couldn't help but wonder what would have happened if Bones hadn't rejected him. Would he have been happy? Would he have been whole? The Special Agent shook his head as he walked up to his partner's office. Even if she had rejected him he wanted to see her one last time before he left.

He groaned when he arrived to an empty office. _Of course she couldn't be here. She always has to make things difficult._ Logically, he knew that it was nearing midnight but he didn't really care at the moment. Booth pulled out his phone and hit the number one speed-dial. Bones's number had had that spot a few months after he had started to work with her. He jumped in surprise when a phone went off in time with the rings on his.

The ex-sniper slowly walked to the desk and saw Bones's high-tech phone flashing _BOOTH_ for the caller ID. He ended the call and picked up his partner's phone. _1 Missed Call_ flashed across the screen and Booth told the phone to ignore it. His gut was telling him that something was wrong. There was no way that she would have left her phone here. Not of her own free will.

Following an instinct he went to recent calls and found that 23:02 Bones had received a call from a restricted number. It had lasted for just over ten minutes. _Who would Bones talk to for ten minutes?_ He couldn't think of an answer. Or at least, not one that led to someone with a restricted phone number.

Booth quickly walked to the security office. "Hi," He paused for a moment to read the guards nametag. "Bernard. Could I take a look at the feeds?"

The man looked up from his magazine to the FBI agent and nodded, waving his hand at the monitors. "Be my guest."

Booth quickly drew up the video from shortly before eleven from the camera that could see into Bones's office and watched it. He noticed that the instant she picked up the phone her face got a frozen look on it. A look she only got when she was afraid. Her facial expressions varied from troubled to out right scared. A few times she looked likes she was going to laugh. When she ended the call she placed the phone on her desk before looking around her office and then walking out.

He felt cold inside. He knew what she was doing. He had done it often enough himself. Whenever he had went on a mission for the Army he had always looked around the barracks in the exact same way that Bones had looked at her office. Like he would never see it again.

The Sergeant Major followed her progress as she left the Jeffersonian. He watched as she talked to a man in a black SUV before climbing into it. Then the car drove away. Seeley Booth was having one hell of a day. And there was only five minutes of it gone.

* * *

><p>Athena followed her escort into the elevator, far more alert than she had been in years. She knew that if this man tried to harm her he would be dead within seconds. It was odd, how quickly she got back into the role of cold-hearted agent. They were in an unofficial CIA base and she was going to see the AD to get debriefed so she could do this job and be done with this life.<p>

There was a slight uneasiness in her gut that said that it wouldn't be that easy, especially if the Agency needed her to come back because they couldn't catch Drake Jr. She ignored the feeling. Feelings got people killed. Feelings made people regret. No emotions meant no hurt. Or at least, that's what she had thought. But then the Squint Squad had changed her opinion of feelings. Well, _Booth_ had changed her opinion of feelings. They weren't just liabilities. They were tools to make one stronger, to allow someone to endure in even the worst of situations. The Dark Angel shook her head as she followed her guide. _Maybe I'm not so cold-hearted after all_.

When her escort gestured at a set of double doors saying, "He's in there." She nodded and walked in without him. There was a long table with a projector on one end and a screen hanging from the wall on the opposite end. Standing by the projector was a man with black hair that was shoulder length who had flashing grey eyes. Jason.

"Hello Athena. I hope your ride was pleasant." His voice was perfectly polite, laced with the etiquette all agents were forced to learn.

"It wasn't. But you already knew that. Just give me the case file and send me on my way so I can get this job over with." Her voice was brisk and business-like but she knew that her old friend could hear her annoyance.

"Still as impatient as ever." He tossed a manila folder on to the table in front of her. "Everything we know about Drake Junior Nero Damon. Which isn't much, to be perfectly honest."

Athena opened the file and saw that he was correct. Date of birth, social security number, high school transcript, permanent record, height, weight, a photo. Nothing that wouldn't be in a normal citizen's folder.

Until she got to the other photos. These were of kids from ages five to twelve all brutally murdered. From the looks of things they had been tortured, stabbed, and then left to die. She felt her insides turn to ice when she saw what was carved into each child's chest. _DARK ANGEL BEWARE._

Drake Jr. was killing these kids to send a message to her. He probably knew that the deaths of innocents would enrage her, force her to come out of retirement. "How long?" She managed to choke out the question from a throat that was twisted with regret and disgust.

Jason looked sympathetic, in an impassive way. Like a doctor saying that a loved one had died and that they were 'very sorry for your loss'. "A few years. We never connected the killings because they were all over the country, and the police never really reported it to us. It was only when one was killed in Carthage, Mississippi that someone reported it to the FBI which then turned it over to us."

Athena felt sick. "The same place that I killed Drake. Who knew to connect me to those murders?"

"Alison Dushane."

"You say that like I should know her." Her voice was calm, even if she felt like screaming on the inside

"You should. She was the girl that Drake held hostage. The one that ended up drenched in his blood."

The Dark Angel closed her eyes. She remembered now.

_She pulled the lifeless form of Drake off of the small girl and saw that she still breathed. There was blood in her hair, all over her body but at least she was alive. Athena pulled the sobbing girl into an embrace. A quick glance confirmed that Drake was really dead with a bullet hole in between his eyes, before she returned her attention to the girl. "Shhh. It's alright now. Shhh. He can't hurt you anymore. Shhh."_

_That was how the local police found the two females. A twenty year-old holding a hysterical six year-old covered in blood. She tried to give the girl to the officers but she only hung on tighter. It was only when her mother came that she released the Agent. As Asheblade walked away from the mother and girl, the girl whispered something unintelligible. Athena turned around and asked, "What was that?"_

_The mother smiled. "She said that you weren't a Dark Angel. That the only thing you could be was just an Angel. You are too kind to be Dark."_

_Athena was stunned. She had just _killed_ a man in front of a six year-old and the girl didn't think that she was dark. The agent didn't even know how that was possible. The blonde girl lifted her head from her mother's shoulder and said, "You'll always be my Angel."_

_The Agent stared at the girl. She had a fierceness in her blue eyes that made Asheblade believe her. The Dark Angel didn't know how to respond to all the emotions that were crashing down over her so she simple whispered, "Thank you." To the girl before walking away._

_Later Athena found out that the girl's name was Alison Dushane. She had never bothered to find out before, she had been so focused on the hunt. The Agent knew that Little Alison would forever be in her mind and heart._

Athena opened her eyes to see Jason watching her with concern. Despite being more emotional due to her stint as Temperance Brennan, she still did not want to discuss her feelings. It just wasn't natural. So she forged ahead, trying to make sense of scattered pieces. "How did Alison see the bodies?"

Jason instantly snapped back into professional mode. "Funny thing that. Apparently she was inspired to become a cop because of a Guardian Angel. You wouldn't happen to know who she meant by that, do you?"

The agent's heart warmed, knowing that the girl still remembered her fondly was one of the greatest gifts anyone could ever give. She had feared that as Alison had grown older she would see what a monster Athena really was. But that apparently wasn't the case.

"I most certainly do not." Was her response. The slight smile on her face said otherwise but Jason knew enough to drop the subject.

"Anyway, Ms. Dushane connected the murders about six months ago and we've been trying to catch Drake Jr. ever since. As you can see, we haven't been very successful. He inherited some of his father's genius, unfortunately."

Athena looked down at the file before again glancing up at Jason. "The last murder was in Erwin, Tennessee so I assume that's where I'm going?"

The Assistant Director of the CIA nodded. "You assumed right." He tossed a bag at her which she caught with ease. "Everything you need."

In the bag was a change of clothes – including tennis shoes – a cell phone, a few hundred dollars, a debit card, a plane ticket to Hensley Airpark, and an ID badge that proudly proclaimed her to be ATHENA ASHEBLADE, CIA.

"There isn't an airport in Erwin, so that's the closest one. The debit card is attached to a bank account with a little less the half a million dollars in it. The pin code is the month and year of when the CIA recruited you."

"In how many digits?"

"Four, two for the month, two for the year."

Athena nodded, showing her understanding. "I'll see you when this bastard's six-feet under or behind bars."

She then turned to leave. "Oh, and Athena?"

The Dark Angel turned back to her superior with a raised eyebrow. "Yes?"

"You should know that your friends are very loyal. They're already looking for you with Seeley Booth leading the charge."

The agent felt a small pang in her theoretical heart at the comment. "Of course they are. He won't give up either."

Jason smiled at his old friend whose face had lit up at the mention of her friends and the FBI agent. "Then solve this case quick so he doesn't obsess about this."

Athena nodded and proudly marched out of the room, toward the waiting flight to some small airport in the middle of nowhere.

* * *

><p>Special Agent Seeley Booth hadn't wasted anytime on calling the Squint Squad together. All of them had been more than a little angry at being awakened at one AM but upon hearing that Brennan was in trouble immediately agreed to come into the Jeffersonian.<p>

That led them to be gathered around monitors in the security office watching as Bones received a phone call and left in an unidentified vehicle. No one knew what was going on.

"So none of you know who would make Bones react like that?"

Angela looked over at him and said quietly, "Booth, we've been over this. We don't know who called her. We don't know why she got into that car. We can't even break the encryption on the stupid number."

And that was what had led to the woman looking so defeated. She was amazing with electronics but couldn't get the number to become un-restricted. She had failed when Brennan appeared to need it most.

Sweets was the next to speak up. "You're probably blaming yourself for not being there, but you shouldn't be. Dr. Brennan is a strong, confident woman and she doesn't need you – "

"I know that Sweets!" Booth shouted.

"I know that." He said more softly. "I just can't shake the feeling that something bad happened to Bones. And I need to know that she's alright. I _need_ to know."

The squint squad all murmured quiet agreements with the ex-sniper's comments. However, with the way that things were looking, it was unlikely that they'd find out what happened to their beloved Bones unless she told them herself.

* * *

><p><strong>Hi, don't expect two updates in one day. I just felt like writing again. Hopefully it's still entertaining, and that it isn't a total bust. I suppose I should also hope that this is original, considering how big this Fandom is. The places might have more meaning to them then random rural towns with populations under 10,000. Or they might not. Only I know at the moment. There's a little bit of gore in this chapter but don't worry if you want more violence, you'll get it...Eventually.<strong>

**Thanks to the two anonymous reviewers: Laval and ANGEL. I hope you both enjoyed this update.**

**Thanks to the lone person who Favorited AIA: NikkiF007.**

**Thanks to those who put AIA on their Alerts list: ****kiwi-094, dana88, .Shadow, KlingonGal8489, and Flaca514.**

**__****_EDIT, 7-5-11: Due to the fact that its better if I focus on one story at a time, this one will be going through a period of no updates, the length depending on however long it takes me to finish one of my other stories...Sorry for that._****__**


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